Prediction, Assessment and Validation of Protein Interaction Maps in Bacteria

High-throughput proteomics technologies, especially the yeast two-hybrid system, produce large volumes of protein–protein interaction data organized in networks. The complete sequencing of many genomes raises questions about the extent to which such networks can be transferred between organisms. We attempted to answer this question using the experimentally derived Helicobacter pylori interaction map and the recently described interacting domain profile pair (IDPP) method to predict a virtual map for Escherichia coli. The extensive literature concerning E. coli was used to assess all predicted interactions and to validate the IDPP method, which clusters protein domains by sequence and connectivity similarities. The IDPP method has a much better heuristic value than methods solely based on protein homology. The IDPP method was further applied to Campylobacter jejuni to generate a virtual interaction map. An in-depth comparison of the chemotaxis pathways predicted in E. coli and C. jejuni led to the proposition of new functional assignments. Finally, the prediction of protein–protein interaction maps across organisms enabled us to validate some of the interactions on the original experimental map.